BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR620534.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 7,128,791
number of mapped reads = 2,952,510 (41.42%)
number of supplementary alignments = 60 (0%)
number of secondary alignments = 0
number of mapped bases = 128,177,704 bp
number of sequenced bases = 128,147,127 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 394,493
duplication rate = 9.05%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.0001
>>>>>>> ACTG content
number of A's = 30,559,993 bp (23.85%)
number of C's = 21,957,324 bp (17.13%)
number of T's = 46,362,024 bp (36.18%)
number of G's = 29,260,012 bp (22.83%)
number of N's = 7,774 bp (0.01%)
GC percentage = 39.97%
>>>>>>> Mismatches and indels
general error rate = 0.0092
number of mismatches = 1,163,312
number of insertions = 7,810
mapped reads with insertion percentage = 0.26%
number of deletions = 20,727
mapped reads with deletion percentage = 0.7%
homopolymer indels = 47.3%
>>>>>>> Coverage
mean coverageData = 0.0414X
std coverageData = 0.6711X
There is a 3.19% of reference with a coverageData >= 1X
There is a 0.53% of reference with a coverageData >= 2X
There is a 0.15% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 11072289 0.04442231259275378 0.9826123483967131
chr2 243199373 9059932 0.03725310591158473 0.45616901898850887
chr3 198022430 9147141 0.046192449006913 0.36713863258431895
chr4 191154276 9070378 0.04745056291599776 0.5739887448264155
chr5 180915260 8328220 0.04603381715837569 0.31836562471043983
chr6 171115067 7990655 0.0466975535240272 0.3838714535545036
chr7 159138663 7511509 0.04720103121640528 1.7324103330213823
chr8 146364022 6749331 0.04611332011633296 0.6287121474615515
chr9 141213431 5596029 0.03962816398108761 0.6107658848898434
chr10 135534747 5920944 0.043685801103092774 0.43290370290916197
chr11 135006516 6071544 0.04497222934039717 0.753601572157958
chr12 133851895 5977658 0.04465874764044245 0.36839277040788576
chr13 115169878 4332226 0.03761596413256598 0.34447103823451486
chr14 107349540 3981179 0.037086130038377435 0.30248147057572167
chr15 102531392 3528204 0.034410963619805335 0.37233743222682286
chr16 90354753 3261304 0.036094437666162396 0.2822533972286523
chr17 81195210 3181397 0.039182077366386514 0.37572070849137706
chr18 78077248 3593860 0.04602954243469237 1.075468988888307
chr19 59128983 2115731 0.03578162337072498 0.5484900109680051
chr20 63025520 2493267 0.039559641872054366 0.37231156361793977
chr21 48129895 1632016 0.033908571793061254 0.36893305721823494
chr22 51304566 1212118 0.023625928343297943 0.2524748895962684
chrMT 16571 500844 30.22412648602981 34.21183691298101
chrX 155270560 4887439 0.03147692002914139 0.5169729805605686
chrY 59373566 962489 0.016210732567418975 0.19275592248227713